[English] 日本語
Yorodumi
- EMDB-80643: Cryo-EM structure of the local tail of bacteriophage A1002 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-80643
TitleCryo-EM structure of the local tail of bacteriophage A1002
Map data
Sample
  • Complex: Pseudomonas aeruginosa phage A1002
    • Protein or peptide: Structural protein
Keywordsphage / VIRAL PROTEIN
Function / homologyStructural protein
Function and homology information
Biological speciesPseudomonas phage (virus) / Pseudomonas phage KPP25 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen Y / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the local tail of bacteriophage A1002
Authors: Chen Y / Liu HR
History
DepositionApr 29, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_80643.png

Downloads & links

-
Map

FileDownload / File: emd_80643.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 160 pix.
= 265.6 Å		1.66 Å/pix.
x 160 pix.
= 265.6 Å		1.66 Å/pix.
x 160 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.35
Minimum - Maximum-6.583337 - 12.425196
Average (Standard dev.)0.0030001167 (±0.6125953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_80643_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_80643_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pseudomonas aeruginosa phage A1002

EntireName: Pseudomonas aeruginosa phage A1002
Components
  • Complex: Pseudomonas aeruginosa phage A1002
    • Protein or peptide: Structural protein

-
Supramolecule #1: Pseudomonas aeruginosa phage A1002

SupramoleculeName: Pseudomonas aeruginosa phage A1002 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage (virus)

-
Macromolecule #1: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage KPP25 (virus)
Molecular weightTheoretical: 67.754844 KDa
SequenceString: MANGLRKTGQ TNTFPERPPV PGRPAYCYVE RRIVPNVNGG QPIGDDYFGS HNANSATNSG SYTVGVPQYT DKVPQYTSMW KVVDVTICV PAVPSEPGIP GKTIVDPKTG WNAGGRSVTA VEGDAILKFT VPDKPTGVLV GFSDGRFDNS FGHPTHAFAF Y PDRFRIYD ...String:
MANGLRKTGQ TNTFPERPPV PGRPAYCYVE RRIVPNVNGG QPIGDDYFGS HNANSATNSG SYTVGVPQYT DKVPQYTSMW KVVDVTICV PAVPSEPGIP GKTIVDPKTG WNAGGRSVTA VEGDAILKFT VPDKPTGVLV GFSDGRFDNS FGHPTHAFAF Y PDRFRIYD RGVIIFEDFF RFTNRYAMSR VGGRVTFYEV NPNDDSSLRP IVNGITPSGG TIYADATLYS VGDFVNDPSF GG NSSAQLN ALVPRLRPTI YEATYAGVDS ELPRMVLVAD AVEPQVINGI VPMPLGNISN YSGATLVRTL PRLVLQAGTS DFV APWSYV SAHIPRPFGS TTILTGEVLG LDNTIPTPQR LISDRPYAEA GGKWPSRYII DVWENLWPPG TLMVPEPMPV YSTA MLDAP VLLMVTDGME ISGTIDLIML VSLDAYDYLG LNTTFTLEST IELMMRDGLA VYSNISTARE TALQYAVNVL TGALT TYQN FGFTGFARVG NDTFGIKNDG LYRLEGETDD GELLRALIDF GADDYGVKNT KRLSSAYAGI TTDGRVYFRI TGDDGE ERV YTLAGESPEF RTPDGVAKGV AARHWRLRLE VEDASFADLD NIEVEVGVSS RRIHRRN

UniProtKB: Structural protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12756
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more